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I am following a great introductory biology course online, MITx: 7.00x on edX.

A question in the course assumes a cross between a pure-breeding male fly and a pure-breeding female fly:

You are studying genetics in a hypothetical fly and you find a fly that has purple eyes. Assume that the purple eye phenotype is due to a mutation at a single locus. Use the notation E and e, where the upper case letter is used for the allele associated with the dominant phenotype and the lower case letter for the allele associated with the recessive phenotype.

You cross a pure-breeding male fly with purple eyes to a pure-breeding female fly with normal eyes. All of the F1 offspring have normal eyes. From this experiment you determine that the purple eye phenotype is ______________ to the normal eye phenotype.

My question is this: how can a male fly be pure-breeding? The reason I wonder is that as far as I understand, pure-breeding implies a homozygote gene, yet the sex chromosome can not be homozygote because the Y chromosome is not homologous to the X chromosome. In other words, does it make sense to speak of homologous sex chromosomes?

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How can a male fly be pure-breeding?

A fly or any organism can only be pure-breeding for a certain trait, not all traits at once. If the trait-determinant allele is found on an autosomal chromosome, this is not a problem. If it's on a sex-chromosome (chr1 in flies), it is sex-linked, and therefore cannot be pure-breeding because it may depend on the sex of the offspring whether the trait is expressed. For instance, you may have a male carrying an allele on its X chromosome; its female offspring will inherit the X, but male offspring will not (those inherit the Y chromosome), i.e. it is not pure-breeding. Male flies cannot be pure-breeding for traits determined by loci on their sex chromosomes. Similarly, you may have a heterozygous female carrying an allele on one of its X chromosomes (A/a); its female offspring will only inherit one allele, either A or a, so it is not pure-breeding either. A female fly must be homozygous for an allele on its sex chromosomes to be pure-breeding for that trait.

Male flies can be pure-breeds for traits determined by alleles on autosomes.

Also, cool and useful funfact, Drosophila sp. male flies do not experience homologous recombination during meiosis. This is called achiasmy! This is useful to know when designing complicated crosses when there is a difficulty in balancing a genotype.

Does it make sense to speak of homologous sex chromosomes?

The X chromosomes in females (X + X) are homologous, but the male Y chromosome is not homologous to the X. They are vastly different, just like the X and Y sex chromosomes in humans.

Pure-breeding implies a homozygote gene

Correct. Pure-breeds are allele homozygous so that all offspring, regardless of recombination, inherit the allele.

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    $\begingroup$ Thank you so much! It all makes more sense now. $\endgroup$ – conciliator Mar 5 at 12:01
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To add to @S Pr's answer and provide another cool and useful fact, in some organisms, like birds, the males are the homomorphic sex (their sex chromosomes are the same size and haven't decayed like the Y has in human males), not the females (who are ZW, with the W being the analogue of the mammalian Y chromosome).

So more generally, sex chromosomes can be homologous only in those organisms which are members of the homomorphic sex, which otherwise phrased means they're homogametic organisms. This sex is female (for mammals).

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